generated: '2026-10-16T22:53:03' study: serinales_vs_pichiales_v2 script: path: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/enrich_novelties_v2.py sha256: d1e8fe16f6842e86fb6c226f822c8c173450a8fec660ca6879a6f8a821ad5aa7 command: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/.pixi/envs/default/bin/python3 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/enrich_novelties_v2.py --results /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2 --config /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/config.csv --annotations /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations --study serinales_vs_pichiales_v2 --cache-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/analysis/enrichment/outputs/cache --threads 8 --pfam-dat /srv/projects/db/pfam/2026-01-27-Pfam38.2/Pfam-A.hmm.dat --interpro-entries /srv/projects/db/interproscan/6.0.0/110.0/interpro/110.0/entries.json --controls /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/zoosporic_dikarya/analysis/enrichment/actin_controls.tsv --ingroup-min-frac 0.75 --universe proteome --cluster-background --out-dir /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/analysis/enrichment/outputs/proteome_clustered class: ephemeral analysis output (not tracked; regenerate with the command above) direction: novelty target_group: label: IN species: - Candalbi - Loddelon - Meyeguil - Debahans - Schestip - Spatpass - Candtenu - Diutrugo - Yamajaro - Candauri - Clavlusi - Metsbicu - Lizaspar other_group: label: OUT species: - Babjinos - Komaphaf - Kuracaps - Pichmemb - Pichkudr - Bretnaar - Ogatpoly - Pachtann - Sacccere - Kluylact - Lachther - Candglab - Torudelb universe: proteome annotations: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations annotation_files: Candalbi: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000000559.tsv.gz Loddelon: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000001996.tsv.gz Meyeguil: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000001997.tsv.gz Debahans: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000000599.tsv.gz Schestip: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000002258.tsv.gz Spatpass: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000000709.tsv.gz Candtenu: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000000707.tsv.gz Diutrugo: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000449547.tsv.gz Yamajaro: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP001152531.tsv.gz Candauri: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000230249.tsv.gz Clavlusi: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000007703.tsv.gz Metsbicu: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000092555.tsv.gz Lizaspar: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000790833.tsv.gz Babjinos: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000094336.tsv.gz Komaphaf: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000000314.tsv.gz Kuracaps: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000019384.tsv.gz Pichmemb: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000094455.tsv.gz Pichkudr: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000249293.tsv.gz Bretnaar: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000290900.tsv.gz Ogatpoly: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000788993.tsv.gz Pachtann: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000094236.tsv.gz Sacccere: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000002311.tsv.gz Kluylact: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000000598.tsv.gz Lachther: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000002036.tsv.gz Candglab: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000002428.tsv.gz Torudelb: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/annotations/UP000005627.tsv.gz annotation_sources: Candalbi: not recorded (no sidecar) Loddelon: not recorded (no sidecar) Meyeguil: not recorded (no sidecar) Debahans: not recorded (no sidecar) Schestip: not recorded (no sidecar) Spatpass: not recorded (no sidecar) Candtenu: not recorded (no sidecar) Diutrugo: not recorded (no sidecar) Yamajaro: not recorded (no sidecar) Candauri: not recorded (no sidecar) Clavlusi: not recorded (no sidecar) Metsbicu: not recorded (no sidecar) Lizaspar: not recorded (no sidecar) Babjinos: not recorded (no sidecar) Komaphaf: not recorded (no sidecar) Kuracaps: not recorded (no sidecar) Pichmemb: not recorded (no sidecar) Pichkudr: not recorded (no sidecar) Bretnaar: not recorded (no sidecar) Ogatpoly: not recorded (no sidecar) Pachtann: not recorded (no sidecar) Sacccere: not recorded (no sidecar) Kluylact: not recorded (no sidecar) Lachther: not recorded (no sidecar) Candglab: not recorded (no sidecar) Torudelb: not recorded (no sidecar) vocabulary_coverage: pfam: species_with_terms: - Candalbi - Loddelon - Meyeguil - Debahans - Schestip - Spatpass - Candtenu - Diutrugo - Yamajaro - Candauri - Clavlusi - Metsbicu - Lizaspar species_without_terms: [] n_with: 13 n_species: 13 pfam_clan: species_with_terms: - Candalbi - Loddelon - Meyeguil - Debahans - Schestip - Spatpass - Candtenu - Diutrugo - Yamajaro - Candauri - Clavlusi - Metsbicu - Lizaspar species_without_terms: [] n_with: 13 n_species: 13 interpro: species_with_terms: - Candalbi - Loddelon - Meyeguil - Debahans - Schestip - Spatpass - Candtenu - Diutrugo - Yamajaro - Candauri - Clavlusi - Metsbicu - Lizaspar species_without_terms: [] n_with: 13 n_species: 13 go: species_with_terms: - Candalbi - Loddelon - Meyeguil - Debahans - Schestip - Spatpass - Candtenu - Diutrugo - Yamajaro - Candauri - Clavlusi - Metsbicu - Lizaspar species_without_terms: [] n_with: 13 n_species: 13 parameters: min_bg: 5 exclude_iea: false report_ids_fdr: 0.05 ingroup_min_frac: 0.75 other_max_frac: 0.0 cluster_background: true statistics: one-sided hypergeometric scipy.stats.hypergeom.sf(k-1,M,n,N); BH (lib/stats_util.bh_fdr) within scope x level x vocabulary; scope-B fdr_bh_all_species = BH across species tests of one level x vocabulary. goatools only parses the OBO and gives is_a ancestors. candidate_check: matrix_in_rule_and_0_out: 1864 candidates_txt: 1864 symmetric_difference: 0 candidates_file: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/candidates.txt presence_matrix: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/presence_matrix.uniprot.tsv rule: IN count / 13 >= 0.75 and OUT count / 13 <= 0.0 (own proteome counts toward the target group) only_in_matrix_rule: [] only_in_candidates_file: [] background_clustering: key: c2e2aaa891a31d60 n_sequences: 73331 n_clusters: 18151 mmseqs: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/.pixi/envs/default/bin/mmseqs mmseqs_version: 18.8cc5c command: mmseqs easy-cluster --threads N --min-seq-id 0.3 -c 0.8 --cov-mode 0 runtime_s: 45.4 threads: 8 created: '2026-10-16T22:52:47' cache_hit: false pipeline_candidate_families: 'novelties..tsv family_id (nf_NovInvenio MMSEQS_CLUSTER: mmseqs easy-cluster --min-seq-id 0.3 -c 0.8 --cov-mode 0 on candidates.fa)' candidates_without_family_row: 0 go_obo: path: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/data/go/go-basic.obo data_version: releases/2026-07-26 sha256: b08d45b268b8c24ccb2513dbbbc7d4df9f6521c099b413f79eb31e06e0fa3bcc pfam_dat: path: /srv/projects/db/pfam/2026-01-27-Pfam38.2/Pfam-A.hmm.dat sha256: ead9a40cdb871e1e6ceb151ea15c7aeaff083add2558031b4811afb9d7496b2d release_note: release taken from directory name; the .dat file has no version line interpro_entries: /srv/projects/db/interproscan/6.0.0/110.0/interpro/110.0/entries.json inputs_sha256: /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/config.csv: 85a71d46e3871a66aace8b86654dbd5f37f2bcb71d5e5910367fa9b4aa59d9b8 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/candidates.txt: 759bd6e8744fa1c198dbce5ea9f645b1c246ffb73f5412fe20baaa8884aed0de /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Candalbi.tsv: 3eccd1e9291b9a4f15a34b2f9800bb9b1046e012e691614da6ea6b231d73eab7 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Loddelon.tsv: bfbb345c965c74fae4d7722b554410739f378d1d5a3870470e81fef67ec168a3 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Meyeguil.tsv: ee412e2c6293357f6e874383a26196d6e45ea0f07a78cbd6d3462570f758b873 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Debahans.tsv: c28efbc2f7a4e30b651cfc7c36809add6e8b23de6cacaac52d87f5581225ec74 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Schestip.tsv: 803b399938b7c921d74961175b794e7c03ec2efd249e8f65bb09e3046fe215a6 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Spatpass.tsv: fa7fa0466a2775f229c692042b8c35695f07d34314597b964353c9ae021ab59a /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Candtenu.tsv: 9e38374004639b4e270585e89e4428a04913a88b874a34706adbaa0637aa9862 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Diutrugo.tsv: 1d9dbd0049e655a651b6c1cf210f15a901bf2f0a39c65239600fadc668a0ef7b /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Yamajaro.tsv: 84bf3e64bc648d5ec99b701eadb5a7b1bc08f23c2833082a1bc43e469cf40f9f /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Candauri.tsv: c81cf96b212792e91fcd23b0e5fd01597057b2c546ae2ba525d66e8d5523f680 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Clavlusi.tsv: f07d7687ac0f7e88f1898789941fd3fb7074b692f3f1bf2f4dac5d9eec8af987 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Metsbicu.tsv: 46bbcba4c8037d489cc9bf76e8ffeeda269dc6b27a552a0d56949979160354f3 /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/novelties.Lizaspar.tsv: 43e8c4c33454ea53060646a2ac9a444bd9beac32598e70433f2e4f78b1b4baf6 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/results/serinales_vs_pichiales_v2/presence_matrix.uniprot.tsv : db9ae2079719672815bebbb736584ef4f83568201f53c13b25866036f2e5f449 ? /bigdata/stajichlab/jstajich/projects/NovInvenio_Investigations/studies/fungi/serinales_vs_pichiales_v2/data_dir/pep/UP000000559_237561.pep.fa : 603def324372fc7aab183f6d4cf3a482c1e97a43e99f018b0d96d47011832090 ? 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